15-23440775-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001304388.2(GOLGA6L2):c.1700G>A(p.Gly567Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000362 in 1,437,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001304388.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOLGA6L2 | NM_001304388.2 | c.1700G>A | p.Gly567Glu | missense_variant | 8/8 | ENST00000567107.6 | |
GOLGA6L2 | XM_047432396.1 | c.1541G>A | p.Gly514Glu | missense_variant | 6/6 | ||
GOLGA6L2 | XM_047432397.1 | c.1228-249G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA6L2 | ENST00000567107.6 | c.1700G>A | p.Gly567Glu | missense_variant | 8/8 | 5 | NM_001304388.2 | P1 | |
GOLGA6L2 | ENST00000566571.5 | c.*981G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 149948Hom.: 0 Cov.: 35
GnomAD4 exome AF: 0.0000388 AC: 50AN: 1287412Hom.: 0 Cov.: 44 AF XY: 0.0000376 AC XY: 24AN XY: 638958
GnomAD4 genome AF: 0.0000133 AC: 2AN: 149948Hom.: 0 Cov.: 35 AF XY: 0.0000273 AC XY: 2AN XY: 73226
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at